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Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Ctrl+Shift+Enter. # Cellchat

CellChat

配体-受体+辅因子

df.net

Registered S3 method overwritten by 'cli':
  method     from    
  print.boxx spatstat

cellchat可视化

# pheatmap(mat, display_numbers = FALSE, number_color ="black", cluster_rows = FALSE, 
         # cluster_cols = FALSE, color = colorRampPalette(c("#1E90FF", "white", "#ff2121"))(400), border_color = NA)
table(cor@idents)

       EC1      SMC_3    Mod_SMC Macrophage    T_cell1      SMC_0      SMC_2    T_cell2    T_cell3        EC2 
      4798       1021       1224       9832      12245       3430       1590       4125        366       1294 
    B_cell  Mast_cell      SMC_1 
      2206        430       2294 

mod_SMC – ACKR3

#chord plot
## 免疫细胞 c(4,5,8,9,11) 和SMC c(2,3,6,7,13)的关系
netVisual_chord_gene(cor, sources.use = c(4,5,8,9,11), targets.use = c(2,3,6,7,13), lab.cex = 0.5, legend.pos.y = 30)

##SMC内部
netVisual_chord_gene(cor, sources.use = c(7,13), targets.use = c(2,3,6), lab.cex = 0.5, legend.pos.y = 30)

#指定pathway
pathways.show <- c("TNF") 
# Hierarchy plot
vertex.receiver = c(2,3,6,7,13) # a numeric vector. 
netVisual_aggregate(cor, signaling = pathways.show, layout = "hierarchy", vertex.receiver = vertex.receiver)

netVisual_aggregate(cor, signaling = pathways.show, layout = "circle")

# netVisual_aggregate(cor, signaling = pathways.show, layout = "chord")

# Heatmap
netVisual_heatmap(cor, signaling = pathways.show, color.heatmap = c("#f1f1f1", "#ff2121"))

Do heatmap based on a single object 

#可视化单个配体受体对的影响
netAnalysis_contribution(cor, signaling = pathways.show)

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